The city missed a deadline Tuesday to fix 16 homeless shelters, including The Auburn Family Residence in Fort Greene, Brooklyn.

The city blew a deadline Tuesday to fix up more than a dozen dangerous and decrepit family shelters — and now faces a loss of millions of dollars in state aid.

On April 28, Gov. Cuomo gave the de Blasio administration seven business days to remedy dozens of serious building and housing code violations at the shelters, ranging from vermin to fire safety violations.

By the Tuesday deadline, the city Department of Homeless Services had yet to address the situation at 16 shelters across the city that house families with children.

“The violations range from severe electrical and plumbing issues that have gone uncorrected for a significant period of time...in direct violation of the building code,” Sharon Devine, executive deputy commissioner of the state Office of Temporary and Disability Assistance, wrote in a letter to city DHS Commissioner Gilbert Taylor.

Several shelters now house families “despite serious structural issues that could endanger their health,” including 12 with fire safety issues, Devine wrote.

The 16 were among 25 red-flagged in March by the city Department of Investigation for hundreds of serious code violations, including dead rats and blocked fire exits.

The state provides the city with $635 million toward homeless aid. Because DHS failed to meet the deadline, on Tuesday the state began withholding funds for the 16 problem shelters.

On Monday, Mayor de Blasio held a press conference outside a Queens shelter to announce he’d formed a task force to clean up the shelter system.

The homeless census in the city has grown to record levels, peaking near 60,000 in December and dropping down to 56,000 this week.

In response, Taylor slapped back at the Cuomo administration, stating, " Instead of spending scarce resources to re-inspect shelters and issue redundant reports, while citing issues which it knows are already being addressed as an excuse to withhold needed funding, the State should be meeting its own fiscal responsibility to New York City’s homeless families."